8VOQ Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8VOQ_025 | 1/D/897:902 | GNRA | geometric HL_4LFB_020 HL_34789.1 | |
| HL_8VOQ_051 | 1/a/566:575 | T-loop with 2 stacked bulged bases | geometric HL_5J7L_150 NA | |
| HL_8VOQ_056 | 1/a/779:785 | No text annotation | geometric HL_5J7L_156 NA | |
| HL_8VOQ_076 | 1/a/1777:1787 | No text annotation | geometric HL_5J7L_178 NA | |
| HL_8VOQ_090 | 1/a/2594:2599 | GNRA | geometric HL_4V9F_065 HL_34789.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8VOQ_001 | No text annotation | ||
| HL_8VOQ_002 | No text annotation | ||
| HL_8VOQ_003 | T-loop with 2 stacked bulged bases | ||
| HL_8VOQ_004 | No text annotation | ||
| HL_8VOQ_005 | No text annotation | ||
| HL_8VOQ_006 | T-loop with 2 stacked bulged bases | ||
| HL_8VOQ_007 | No text annotation | ||
| HL_8VOQ_008 | No text annotation | ||
| HL_8VOQ_009 | GNRA | ||
| HL_8VOQ_010 | GNRA | ||
| HL_8VOQ_011 | No text annotation | ||
| HL_8VOQ_012 | GNRA related | ||
| HL_8VOQ_013 | GNRA | ||
| HL_8VOQ_014 | No text annotation | ||
| HL_8VOQ_015 | UNCG | ||
| HL_8VOQ_016 | GNRA | ||
| HL_8VOQ_017 | UNCG | ||
| HL_8VOQ_018 | GNRA wlth extra near cWW | ||
| HL_8VOQ_019 | GNRA-like with tWH | ||
| HL_8VOQ_020 | No text annotation | ||
| HL_8VOQ_021 | GNRA | ||
| HL_8VOQ_022 | No text annotation | ||
| HL_8VOQ_023 | No text annotation | ||
| HL_8VOQ_024 | GNRA | ||
| HL_8VOQ_026 | GNRA | ||
| HL_8VOQ_027 | GNRA | ||
| HL_8VOQ_028 | T-loop related | ||
| HL_8VOQ_029 | No text annotation | ||
| HL_8VOQ_030 | GNRA | ||
| HL_8VOQ_031 | GNRA | ||
| HL_8VOQ_032 | T-loop with 3 stacked bulged bases | ||
| HL_8VOQ_033 | No text annotation | ||
| HL_8VOQ_034 | UNCG | ||
| HL_8VOQ_035 | No text annotation | ||
| HL_8VOQ_036 | No text annotation | ||
| HL_8VOQ_037 | No text annotation | ||
| HL_8VOQ_038 | UNCG | ||
| HL_8VOQ_039 | No text annotation | ||
| HL_8VOQ_040 | No text annotation | ||
| HL_8VOQ_041 | No text annotation | ||
| HL_8VOQ_042 | No text annotation | ||
| HL_8VOQ_043 | T-loop with 2 stacked bulged bases | ||
| HL_8VOQ_044 | No text annotation | ||
| HL_8VOQ_045 | T-loop with unstacked turn | ||
| HL_8VOQ_046 | No text annotation | ||
| HL_8VOQ_047 | Pseudoknot geometry | ||
| HL_8VOQ_048 | GNRA | ||
| HL_8VOQ_049 | GNRA | ||
| HL_8VOQ_050 | No text annotation | ||
| HL_8VOQ_052 | No text annotation | ||
| HL_8VOQ_053 | GNRA | ||
| HL_8VOQ_054 | No text annotation | ||
| HL_8VOQ_055 | GNRA wlth tandem sheared | ||
| HL_8VOQ_057 | No text annotation | ||
| HL_8VOQ_058 | No text annotation | ||
| HL_8VOQ_059 | No text annotation | ||
| HL_8VOQ_060 | No text annotation | ||
| HL_8VOQ_061 | GNRA wlth tandem sheared | ||
| HL_8VOQ_062 | No text annotation | ||
| HL_8VOQ_063 | GNRA | ||
| HL_8VOQ_064 | T-loop with 2 stacked bulged bases | ||
| HL_8VOQ_065 | Pseudoknot geometry with 3' bulge | ||
| HL_8VOQ_066 | GNRA | ||
| HL_8VOQ_067 | No text annotation | ||
| HL_8VOQ_068 | Mini UNCG with extended bulge | ||
| HL_8VOQ_069 | Pseudoknot geometry with 3' bulge | ||
| HL_8VOQ_070 | UNCG | ||
| HL_8VOQ_071 | Mini UNCG | ||
| HL_8VOQ_072 | GNRA | ||
| HL_8VOQ_073 | UNCG | ||
| HL_8VOQ_074 | No text annotation | ||
| HL_8VOQ_075 | No text annotation | ||
| HL_8VOQ_077 | GNRA related | ||
| HL_8VOQ_078 | GNRA variation | ||
| HL_8VOQ_079 | No text annotation | ||
| HL_8VOQ_080 | UNCG | ||
| HL_8VOQ_081 | No text annotation | ||
| HL_8VOQ_082 | No text annotation | ||
| HL_8VOQ_083 | No text annotation | ||
| HL_8VOQ_084 | Pseudoknot geometry | ||
| HL_8VOQ_085 | GNRA | ||
| HL_8VOQ_086 | GNRA | ||
| HL_8VOQ_087 | No text annotation | ||
| HL_8VOQ_088 | No text annotation | ||
| HL_8VOQ_089 | GNRA variation | ||
| HL_8VOQ_091 | GNRA | ||
| HL_8VOQ_092 | Ribsomal LSU H95 | ||
| HL_8VOQ_093 | No text annotation | ||
| HL_8VOQ_094 | No text annotation | ||
| HL_8VOQ_095 | No text annotation | ||
| HL_8VOQ_096 | GNRA | ||
| HL_8VOQ_097 | No text annotation | ||
| HL_8VOQ_098 | No text annotation | ||
| HL_8VOQ_099 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8VOQ_023 | 1/D/569:575, 1/D/880:881 | No text annotation | geometric IL_5J7L_026 NA | |
| IL_8VOQ_035 | 1/D/887:894, 1/D/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | geometric IL_5J7L_038 NA | |
| IL_8VOQ_053 | 1/D/1399:1401, 1/D/1501:1504 | No text annotation | geometric IL_5J7L_058 NA | |
| IL_8VOQ_054 | 1/D/1412:1414, 1/D/1486:1488 | Isolated non-canonical cWW pair | geometric IL_5J7L_061 NA | |
| IL_8VOQ_071 | 1/a/564:566, 1/a/575:577 | Isolated non-canonical cWW pair | geometric IL_5J7L_257 NA | |
| IL_8VOQ_078 | 1/a/738:740, 1/a/757:758 | Major groove platform | geometric IL_5J7L_264 NA | |
| IL_8VOQ_079 | 1/a/741:742, 1/a/754:756 | Single stack bend | geometric IL_8P9A_328 IL_15011.1 | |
| IL_8VOQ_080 | 1/a/742:744, 1/a/753:754 | Single stack bend | geometric IL_4V84_420 NA | |
| IL_8VOQ_081 | 1/a/775:777, 1/a/787:791 | Multiple bulged bases | geometric IL_5J7L_265 NA | |
| IL_8VOQ_106 | 1/a/1262:1269, 1/a/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5J7L_289 NA | |
| IL_8VOQ_126 | 1/a/1666:1674, 1/a/1990:1994 | No text annotation | geometric IL_5J7L_386 NA | |
| IL_8VOQ_127 | 1/a/1669:1674, 1/a/1990:1993 | Intercalated tWH | geometric IL_5J7L_307 NA | |
| IL_8VOQ_141 | 1/a/2070:2071, 1/a/2438:2441 | Minor groove platform | geometric IL_9DFE_081 IL_34520.1 | |
| IL_8VOQ_157 | 1/a/2591:2592, 1/a/2601:2603 | Single bulged A | geometric IL_1U9S_001 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8VOQ_001 | Single bulged G | ||
| IL_8VOQ_002 | Single bulged A | ||
| IL_8VOQ_003 | No text annotation | ||
| IL_8VOQ_004 | Minor groove platform | ||
| IL_8VOQ_005 | Multiple bulged bases | ||
| IL_8VOQ_006 | Minor groove platform with extra cWW | ||
| IL_8VOQ_007 | Minor groove platform | ||
| IL_8VOQ_008 | Single bulged G | ||
| IL_8VOQ_009 | Isolated non-canonical cWW pair | ||
| IL_8VOQ_010 | Minor groove platform related | ||
| IL_8VOQ_011 | No text annotation | ||
| IL_8VOQ_012 | Kink-turn with non-sequential stacking | ||
| IL_8VOQ_013 | No text annotation | ||
| IL_8VOQ_014 | C-loop | ||
| IL_8VOQ_015 | Single bulged U | ||
| IL_8VOQ_016 | C-loop | ||
| IL_8VOQ_017 | Single bulged G | ||
| IL_8VOQ_018 | No text annotation | ||
| IL_8VOQ_019 | No text annotation | ||
| IL_8VOQ_020 | tSH-tHW-tWW | ||
| IL_8VOQ_021 | No text annotation | ||
| IL_8VOQ_022 | SSU/LSU pseudoknot | ||
| IL_8VOQ_024 | tSH-tHW-tHS | ||
| IL_8VOQ_025 | Major groove platform | ||
| IL_8VOQ_026 | Major groove minor groove platform; mini C-loop | ||
| IL_8VOQ_027 | No text annotation | ||
| IL_8VOQ_028 | Major groove platform; stack outside cWW | ||
| IL_8VOQ_029 | Single stack bend | ||
| IL_8VOQ_030 | Tandem non-canonical cWW pairs | ||
| IL_8VOQ_031 | No text annotation | ||
| IL_8VOQ_032 | Kink-turn | ||
| IL_8VOQ_033 | Left turn | ||
| IL_8VOQ_034 | tSH-tHW-tHS | ||
| IL_8VOQ_036 | Single bulged A | ||
| IL_8VOQ_037 | Single bulged G | ||
| IL_8VOQ_038 | Minor groove platform | ||
| IL_8VOQ_039 | Minor groove platform | ||
| IL_8VOQ_040 | Minor groove platform | ||
| IL_8VOQ_041 | No text annotation | ||
| IL_8VOQ_042 | Single bulged U | ||
| IL_8VOQ_043 | Isolated cWS basepair | ||
| IL_8VOQ_044 | Minor groove platform | ||
| IL_8VOQ_045 | Single bulged A | ||
| IL_8VOQ_046 | Isolated non-canonical cWW pair | ||
| IL_8VOQ_047 | No text annotation | ||
| IL_8VOQ_048 | Minor groove platform | ||
| IL_8VOQ_049 | No text annotation | ||
| IL_8VOQ_050 | No text annotation | ||
| IL_8VOQ_051 | No text annotation | ||
| IL_8VOQ_052 | No text annotation | ||
| IL_8VOQ_055 | Double sheared | ||
| IL_8VOQ_056 | Triple sheared related | ||
| IL_8VOQ_057 | Single bulged A | ||
| IL_8VOQ_058 | No text annotation | ||
| IL_8VOQ_059 | Triple sheared with non-canonical cWW | ||
| IL_8VOQ_060 | Single bulged A | ||
| IL_8VOQ_061 | Minor groove platform | ||
| IL_8VOQ_062 | No text annotation | ||
| IL_8VOQ_063 | Single stack bend | ||
| IL_8VOQ_064 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_8VOQ_065 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_8VOQ_066 | No text annotation | ||
| IL_8VOQ_067 | No text annotation | ||
| IL_8VOQ_068 | No text annotation | ||
| IL_8VOQ_069 | No text annotation | ||
| IL_8VOQ_070 | Double sheared | ||
| IL_8VOQ_072 | AAA cross-strand stack | ||
| IL_8VOQ_073 | Isolated non-canonical cWW pair | ||
| IL_8VOQ_074 | tHW-tHW cross-strand stack | ||
| IL_8VOQ_075 | Single bulged A | ||
| IL_8VOQ_076 | Single bulged G | ||
| IL_8VOQ_077 | Triple sheared | ||
| IL_8VOQ_082 | 90 degree turn | ||
| IL_8VOQ_083 | No text annotation | ||
| IL_8VOQ_084 | Stack outside cWW | ||
| IL_8VOQ_085 | Single stack bend | ||
| IL_8VOQ_086 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_8VOQ_087 | Single bulged G | ||
| IL_8VOQ_088 | C-loop with bulged stacked A's | ||
| IL_8VOQ_089 | Isolated non-canonical cWW pair | ||
| IL_8VOQ_090 | Double sheared with non-canonical cWW | ||
| IL_8VOQ_091 | No text annotation | ||
| IL_8VOQ_092 | Single bulged C | ||
| IL_8VOQ_093 | UAA/GAN | ||
| IL_8VOQ_094 | SSU/LSU pseudoknot | ||
| IL_8VOQ_095 | Single bulged U | ||
| IL_8VOQ_096 | Kink-turn related | ||
| IL_8VOQ_097 | No text annotation | ||
| IL_8VOQ_098 | Isolated non-canonical cWW pair | ||
| IL_8VOQ_099 | Tandem non-canonical cWW pairs | ||
| IL_8VOQ_100 | Kink-turn | ||
| IL_8VOQ_101 | No text annotation | ||
| IL_8VOQ_102 | Major groove platform | ||
| IL_8VOQ_103 | Isolated cWS basepair | ||
| IL_8VOQ_104 | No text annotation | ||
| IL_8VOQ_105 | Kink-turn | ||
| IL_8VOQ_107 | Major groove platform; stack outside cWW | ||
| IL_8VOQ_108 | C-loop | ||
| IL_8VOQ_109 | UAA/GAN | ||
| IL_8VOQ_110 | tSH-tHW-tHS | ||
| IL_8VOQ_111 | Single stack bend | ||
| IL_8VOQ_112 | Single stack bend | ||
| IL_8VOQ_113 | No text annotation | ||
| IL_8VOQ_114 | UAA/GAN | ||
| IL_8VOQ_115 | Tandem non-canonical cWW pairs | ||
| IL_8VOQ_116 | tSH-tHW | ||
| IL_8VOQ_117 | Single bulged U | ||
| IL_8VOQ_118 | No text annotation | ||
| IL_8VOQ_119 | tSH-tHW-tHS | ||
| IL_8VOQ_120 | 180 degree turn | ||
| IL_8VOQ_121 | Single bulged A | ||
| IL_8VOQ_122 | UAA/GAN variation | ||
| IL_8VOQ_123 | No text annotation | ||
| IL_8VOQ_124 | Isolated tWW turn | ||
| IL_8VOQ_125 | Major groove platform; stack outside cWW | ||
| IL_8VOQ_128 | tSH-tSH-tHH-tHS | ||
| IL_8VOQ_129 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_8VOQ_130 | Triple sheared | ||
| IL_8VOQ_131 | Single bulged A | ||
| IL_8VOQ_132 | Kink-turn related | ||
| IL_8VOQ_133 | Minor groove platform, major groove intercalation | ||
| IL_8VOQ_134 | Major groove intercalation | ||
| IL_8VOQ_135 | Major groove minor groove platform; mini C-loop | ||
| IL_8VOQ_136 | No text annotation | ||
| IL_8VOQ_137 | UAA/GAN related | ||
| IL_8VOQ_138 | Bulged stacked bases | ||
| IL_8VOQ_139 | Major groove platform | ||
| IL_8VOQ_140 | No text annotation | ||
| IL_8VOQ_142 | Isolated tHS basepair with bulges | ||
| IL_8VOQ_143 | Isolated non-canonical cWW pair | ||
| IL_8VOQ_144 | Isolated non-canonical cWW pair | ||
| IL_8VOQ_145 | Isolated non-canonical cWW pair | ||
| IL_8VOQ_146 | No text annotation | ||
| IL_8VOQ_147 | No text annotation | ||
| IL_8VOQ_148 | Kink-turn | ||
| IL_8VOQ_149 | Single bulged U | ||
| IL_8VOQ_150 | Double sheared | ||
| IL_8VOQ_151 | No text annotation | ||
| IL_8VOQ_152 | Major groove minor groove platform with extra cWW | ||
| IL_8VOQ_153 | Double sheared with non-canonical cWW | ||
| IL_8VOQ_154 | Isolated non-canonical cWW with bulges | ||
| IL_8VOQ_155 | No text annotation | ||
| IL_8VOQ_156 | Major groove platform with intercalation | ||
| IL_8VOQ_158 | tSH-tHS-tHW | ||
| IL_8VOQ_159 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_8VOQ_160 | C-loop | ||
| IL_8VOQ_161 | UAA/GAN related, with intercalation | ||
| IL_8VOQ_162 | Multiple bulged bases | ||
| IL_8VOQ_163 | UAA/GAN with extra cWW | ||
| IL_8VOQ_164 | No text annotation | ||
| IL_8VOQ_165 | Major groove intercalation | ||
| IL_8VOQ_166 | Multiple bulged bases with non-canonical cWW | ||
| IL_8VOQ_167 | tHS double platform | ||
| IL_8VOQ_168 | Major groove intercalation | ||
| IL_8VOQ_169 | No text annotation | ||
| IL_8VOQ_170 | Major groove minor groove platform; mini C-loop | ||
| IL_8VOQ_171 | Symmetric double minor groove platform | ||
| IL_8VOQ_172 | Bacterial 5S Loop E |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8VOQ_022 | 1/a/683:689, 1/a/773:775, 1/a/791:794 | No text annotation | geometric J3_5J7L_038 NA | |
| J4_8VOQ_005 | 1/D/575:577, 1/D/764:769, 1/D/810:821, 1/D/879:880 | No text annotation | ||
| J5_8VOQ_005 | 1/a/531:533, 1/a/560:564, 1/a/577:579, 1/a/1261:1262, 1/a/2017:2018 | No text annotation | ||
| J5_8VOQ_006 | 1/a/584:589, 1/a/668:671, 1/a/809:812, 1/a/1195:1196, 1/a/1250:1256 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_8VOQ_001 | No text annotation | ||
| J3_8VOQ_002 | No text annotation | ||
| J3_8VOQ_003 | No text annotation | ||
| J3_8VOQ_004 | No text annotation | ||
| J3_8VOQ_005 | No text annotation | ||
| J3_8VOQ_006 | No text annotation | ||
| J3_8VOQ_007 | No text annotation | ||
| J3_8VOQ_008 | No text annotation | ||
| J3_8VOQ_009 | No text annotation | ||
| J3_8VOQ_010 | No text annotation | ||
| J3_8VOQ_011 | No text annotation | ||
| J3_8VOQ_012 | No text annotation | ||
| J3_8VOQ_013 | No text annotation | ||
| J3_8VOQ_014 | No text annotation | ||
| J3_8VOQ_015 | No text annotation | ||
| J3_8VOQ_016 | No text annotation | ||
| J3_8VOQ_017 | No text annotation | ||
| J3_8VOQ_018 | No text annotation | ||
| J3_8VOQ_019 | No text annotation | ||
| J3_8VOQ_020 | No text annotation | ||
| J3_8VOQ_021 | No text annotation | ||
| J3_8VOQ_023 | No text annotation | ||
| J3_8VOQ_024 | No text annotation | ||
| J3_8VOQ_025 | No text annotation | ||
| J3_8VOQ_026 | No text annotation | ||
| J3_8VOQ_027 | No text annotation | ||
| J3_8VOQ_028 | No text annotation | ||
| J3_8VOQ_029 | Kink-turn 3-way junction | ||
| J3_8VOQ_030 | No text annotation | ||
| J3_8VOQ_031 | No text annotation | ||
| J3_8VOQ_032 | No text annotation | ||
| J3_8VOQ_033 | No text annotation | ||
| J3_8VOQ_034 | No text annotation | ||
| J3_8VOQ_035 | No text annotation | ||
| J4_8VOQ_001 | No text annotation | ||
| J4_8VOQ_002 | No text annotation | ||
| J4_8VOQ_003 | No text annotation | ||
| J4_8VOQ_004 | No text annotation | ||
| J4_8VOQ_006 | No text annotation | ||
| J4_8VOQ_007 | No text annotation | ||
| J4_8VOQ_008 | No text annotation | ||
| J4_8VOQ_009 | No text annotation | ||
| J4_8VOQ_010 | No text annotation | ||
| J4_8VOQ_011 | No text annotation | ||
| J4_8VOQ_012 | No text annotation | ||
| J4_8VOQ_013 | No text annotation | ||
| J4_8VOQ_014 | No text annotation | ||
| J4_8VOQ_015 | No text annotation | ||
| J5_8VOQ_001 | No text annotation | ||
| J5_8VOQ_002 | No text annotation | ||
| J5_8VOQ_003 | No text annotation | ||
| J5_8VOQ_004 | No text annotation | ||
| J5_8VOQ_007 | No text annotation | ||
| J6_8VOQ_001 | No text annotation | ||
| J7_8VOQ_001 | No text annotation | ||
| J7_8VOQ_002 | No text annotation |
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